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· Normal Mode calculation
  · Examples (Movies)
  · Submit a job (from PDB file)
  · Elastic Energy (Perturb. Anal.)
· Overlap coefficients
  · Include Profit step
· Molecular Replacement
  · Split trajectory (for MR)
  · Generate decoys (MixMod)
· X-Ray refinement
  · Standard refinement
  · Screening Mol. Repl. Solns.
· EM refinement
  · Documents/Examples
  · Get Structure Factors
  · Submit a job (no NCS)
  · Submit job with NCS
· Docking refinement
  · Submit a job (refinement)
  · Submit a job (scanning)
· Force field methods
  · Energy minimization
  · Gromacs NMA
· References
· Homes/Links
· Job queue status

Examples of Normal Modes Analysis on large molecular complexes (Movies)

A typical example from Citrate Synthase (6CSC) that is directly readable by PyMol can be found here (mode #7).

Get mode_7.pdb on your disk and install Pymol (downloadable here) if you don't already have it and then type:
pymol mode_7.pdb

and play the movie by using the bottom right menu.

You can get a nicer view by clicking first A in the top right menu, then Preset, then Publication.

Alternatively, you may download and look at the movie with VMD.

Here is an animated-GIF Movie of the same molecule.

Use the following two commands to generate a C-alpha trace movie with PyMOL:
1) pymol mode_1.pdb
Pymol>set cartoon_trace, 1
Pymol>show cartoon
2) Then change colors and play the movie...

  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 19:37 April 19, 2014.